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| Status |
Public on Apr 21, 2021 |
| Title |
Ovotestis mix scRNA-seq |
| Sample type |
SRA |
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| Source name |
Ovotestis
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| Organism |
Monopterus albus |
| Characteristics |
tissue: gonad
age: adult
treatment: untreated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Gonads were collected and washed. Samples were minced with sterilized scissors after washing, then were digested in collagenase type IV, trypsin, and Deoxyribonuclease I. After stopping digestion, single cells were obtained by strainers for library preparation with Chromium single-cell 3′ reagent kits V3.
Chromium single-cell 3′reagent kits V3 were used for scRNA-seq library preparation with Chromium Controller.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Raw sequencing data were demultiplexed using CellRanger (CellRanger v 3.1.0) with default parameters to get Fastq files.
Reads were aligned to reference genome (M_albus_1.0) using STAR of CellRanger.
Barcode and UMI counting were performed to generate feature-barcode matrices by CellRanger count application.
Single cell data was filtered with Seurat package (v3.1.0) with default parameters.
Genome_build: monopterus albus NCBI genome build 1.
Supplementary_files_format_and_content: Matrix table with raw gene UMIs for every gene and every cell.
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| Submission date |
Jul 07, 2020 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Xin Wang |
| E-mail(s) |
wxzbdx2010@126.com
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| Organization name |
Wuhan University
|
| Department |
College of Life Sciences
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| Lab |
4114
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| Street address |
No.299 Bayi Road, Wuchang District
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| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL28839 |
| Series (1) |
| GSE153961 |
Molecular and cellular design of ovotestis development |
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| Relations |
| BioSample |
SAMN15465038 |
| SRA |
SRX8680767 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4661001_barcodes.tsv.gz |
41.4 Kb |
(ftp)(http) |
TSV |
| GSM4661001_genes.tsv.gz |
141.7 Kb |
(ftp)(http) |
TSV |
| GSM4661001_matrix.mtx.gz |
97.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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